We performed exome sequencing on a tissue biopsy of untreated metastatic prostate cancer, a tissue biopsy of castrate resistant prostate cancer with neuroendocrine features, and on whole genome-amplified DNA from multiple pools of circulating tumor cells taken within weeks of the 2nd tissue biopsy. This study demonstrated that pooled CTCs capture the mutational profile of advanced prostate cancer. Moreover, it demonstrated that CTCs collected by targeting an epithelial marker, EpCAM, also capture mutations associated with neuroendocrine disease. A manuscript resulting from this work supports the utility of using CTCs to represent the current genomic characteristics of advanced prostate cancer.